The Publish command is known to set SAVETIME (the sysvar that controls how often and/or IF, autosave fires) to 0 - which turns it off.
But it could be something else too. Go here to find some lisp code that you can load, that will tell you when SAVETIME changes.
At least this way, you'll know that it has changed and may be able to fix whatever is doing it.
But more importantly, get into the habit of pressing Ctrl+S more often while you're working, and chances are you won't need your autosave files.